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Fix write validation against empty transformations - #1118

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LucaMarconato merged 3 commits into
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fix/validate-against-empty-transformations
May 7, 2026
Merged

Fix write validation against empty transformations#1118
LucaMarconato merged 3 commits into
mainfrom
fix/validate-against-empty-transformations

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@LucaMarconato

@LucaMarconatoLucaMarconato commented May 7, 2026•
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The parsers add transformations to empty elements, but after parsing, if a user calls remove_transformation(element, remove_all=True), the transformations dict is set to {} rather than None, bypassing the is-None guard in all three IO writers.

The fix is general: we now call the validators before writing, and we check the presence of transformations in the validator.

LucaMarconatoand others added 2 commits May 7, 2026 10:06
@LucaMarconato@claude
Fix write validation not catching empty (rather than None) transforma…
aea89c5
…tions
After remove_transformation(element, remove_all=True) the transformations
dict is set to {} rather than None, bypassing the is-None guard in all three
IO writers. Changed the check to `not transformations` so both None and empty
dicts are caught, and added a parametrized regression test covering images,
multiscale images, labels, multiscale labels, shapes, and points.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@LucaMarconato@claude
Move empty-transformation validation into model validate() methods
2f18304
Instead of guarding in each IO writer, call get_model(element) (which
already dispatches to the right schema and runs validate()) at the start
of _write_element() for all non-table spatial elements.
Also fix the is-None guards in all three validate() methods to use
`not transformations` / `not data.attrs.get(key)` so that an empty
dict {} is caught in addition to None.
The IO-level guards added in the previous commit are removed since they
are now superseded by the model-level check; assert statements are kept
to narrow the type for mypy.
The regression test is updated to reflect the correct production scenario:
element is already inside a SpatialData object when its transformations are
removed in-place, so the error fires during write() not at construction.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@LucaMarconatoLucaMarconato mentioned this pull request May 7, 2026
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codecovBot commented May 7, 2026•
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Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 92.03%. Comparing base (5ead6cc) to head (8c42cbe).
⚠️ Report is 22 commits behind head on main.

Additional details and impacted files
@@ Coverage Diff @@## main #1118 +/- ##
==========================================
+ Coverage 91.97% 92.03% +0.05% 
==========================================
Files 51 51 Lines 7750 7757 +7 ==========================================
+ Hits 7128 7139 +11 + Misses 622 618 -4
Files with missing linesCoverage Δ
src/spatialdata/_core/spatialdata.py91.95% <100.00%> (+0.02%)⬆️
src/spatialdata/_io/io_points.py100.00% <100.00%> (+2.27%)⬆️
src/spatialdata/_io/io_raster.py93.22% <100.00%> (+1.04%)⬆️
src/spatialdata/_io/io_shapes.py96.15% <100.00%> (+1.21%)⬆️
src/spatialdata/models/__init__.py100.00% <ø> (ø)
src/spatialdata/models/models.py87.97% <100.00%> (+0.16%)⬆️
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@LucaMarconatoLucaMarconato mentioned this pull request May 7, 2026
Merged
@LucaMarconato@claude
Move empty-transformation validation into model validate() methods
8c42cbe
Instead of guarding in each IO writer, call validate_element(element)
(a new public helper in spatialdata.models that delegates to get_model)
at the start of _write_element() for all non-table spatial elements.
Validation changes in models.py:
- RasterSchema._check_transforms_present: two explicit checks —
one for None (key absent) and one for empty dict, with separate messages
- ShapesModel.validate / PointsModel.validate: same split into two checks
- asserts in IO files are kept solely for mypy type-narrowing, each
annotated with a comment explaining that validate_element() guarantees
the invariant at runtime
New public API:
- spatialdata.models.validate_element(e) raises ValueError if the element
fails schema validation; documented in docs/api/models_utils.md
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@LucaMarconato
LucaMarconato marked this pull request as ready for review May 7, 2026 10:31
@LucaMarconato
LucaMarconato enabled auto-merge (squash) May 7, 2026 10:32
@LucaMarconato
LucaMarconato merged commit ef757d1 into mainMay 7, 2026
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@LucaMarconato
LucaMarconato deleted the fix/validate-against-empty-transformations branch May 7, 2026 10:43
@Artur-manArtur-man mentioned this pull request Aug 18, 2026
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